The goals of this project are to develop improved quantitative methods for analysis of genetic data gathered in family and population studies of complex diseases, and to implement these methods in easy to use computer programs. Such methods are required to unravel the complex genetic basis of common diseases. New methods will be developed for the following tasks: Faster and more memory-efficient multi-point analysis of both qualitative and quantitative traits in arbitrarily large and complex pedigrees; Testing haplotypes for association with disease; Multipoint linkage disequilibrium analysis; SNP-based association studies. New technologies are allowing collection of increasingly large amounts of polymorphism data on common disease samples drawn from both families and populations. The new methods developed for this project will enable efficient use of these data, and will improve researchers' ability to detect true genetic effects on disease susceptibility and to distinguish them from statistical noise. The computer programs will be freely distributed to the broader research community to ensure that the methods are widely and readily applied to real-world problems.